I just read your Who Stole Westeros article (great onde, btw!), and it got me thinking: how could the crown undo all the financial damage Littlefinger did?
This is something that I've discussed in bits and pieces, but I think it's a good idea to have one place where I lay out my ideas.
The first thing that needs to happen is that the crown needs to get an accurate understanding of its finances and make that understanding known to the necessary stakeholders. This starts with a very thorough audit of both the Crown's books and Littlefinger's books, preferably done with the participation of the Iron Bank (not only do they have the necessary expertise to see through Baelish's fraud, but bringing them into the process at an early stage will make later negotiations easier because they're more likely to feel "part of the team" and not like a bombshell's been dropped on them).
The second step is, I would argue, a document laying out, in detail, what the Crown's incomes, expenditures, and debts actually are - and the extent of Littlefinger's fraud and embezzlement - is absolutely vital for rebuilding trust from the Crown's major creditors. Think of this as a somewhat more private (and hopefully more honest) Compte Rendu. Not only is having an accurate understanding vital for future policymaking, but it's also a way of framing the overall narrative to your creditors that defines the universe of how much you can afford to pay back and how much you should pay back.
After the full scope of the economic damage is known, the first priority should be to A. recoup as much of the losses as possible, and B. reduce the debt that has to be paid as much as possible. As far as A goes, the absolute de minimus strategy should be to seize the entire Baelish estate - not just the gold, but also the brothels, the ships, the commodities futures, the debts of various noble houses and merchants, the lands and titles belonging to Harrenhal - and those of all of his minions in the royal bureaucracy, and use that to improve the royal income-to-debt ratio by paying off some of what's owed, with as much as possible going to principal over interest.
Secondly, there's a strong need for debt relief. That's a touchy subject around creditors, but it's still one that has to be faced - and is made somewhat easier by the War of Five Kings. So if Renly or Stannis had won, it would absolutely been in their interests to declare the Crown's debt to House Lannister repudiated on the grounds of treason, thus reducing the total owed by 50% (assuming that the Crown actually owes 3 million to House Lannister and 6 million overall). On the flip side, and this is somewhat paradoxical, it is rather surprising that at no point after the death of King Robert does the Lannister regime forgive debt it effectively owes to itself, even if that would be to its ultimate advantage.
Ultimately, though, the nice thing about being a government is that (barring a revolution or foreign conquest) you are effectively immortal, and thus even staggeringly huge debts can be dealt with - over a long enough time horizon. Look at the example of British war debt:
It turns out, constantly fighting imperial wars and then having to fight two world wars is very expensive, but just hanging on as a going concern was enough to gradually reduce the debt-to-gdp ratio down to manageable levels. It really helps if you have a central bank, a sinking fund, and strong levels of economic growth, but just staying alive is the big ticket.
However, in order for time to heal all wounds, one of the things that has to happen is some debt restructuring aimed at reducing the interest rate owed on the royal debt. Pretty much all previous steps I've outlined, from sharing information to cultivating stakeholders to paying off as much as you can from Littlefinger's coffers, etc. are aimed at trying to soften the negotiating ground for this step, because medieval interest rates were really high (largely as a hedge against frequent defaults), around 12% on average. It's pretty hard to grow your way out of that, so bringing down those rates is the top priority. Once you've gotten them as low as you can, you want to negotiate for the longest repayment window possible.